Gender differences in sub-major choices within the science, technology, engineering, and mathematics (STEM) fields have scarcely been discussed. This study uses administrative records from a top medical school in China to examine gender differences in medical students’ specialty choices. Results showed that, although the gender gap in choosing a clinical track shrinks over time, female students in the clinical track are far less likely to choose highly paid surgical specialties, and this gap persists over time. However, female students outperformed male students in all of the courses. Thus, academic performance cannot explain the underrepresentation of female students in surgery. We further collected questions such as “Why don’t female students choose surgical specialties” and answers to them in “Chinese Quora”, Zhihu.com. A preliminary text analysis showed that ultra-physical load, discrimination in recruitment, women-unfriendly work climates, and difficulties in taking care of family are barriers that prevent women from choosing surgery.